Mesenchymal stem cells (MSCs) are a multipotent cell population which have been described to exert renoprotective and regenerative effects in experimental models of kidney injury. In addition, it was recently shown that human MSCs are able to contribute to the development of both renal tubules and glomeruli. These results suggest that MSCs might be potential candidates for stem cell-based de novo renal tissue generation. The current study was aimed at re-evaluating the renogenic capacity of mouse and human bone marrow-derived MSCs. In order to elucidate the renogenic potential of MSCs, a novel method of embryonic kidney culture was used that is based on disaggregation of mouse kidney rudiments and their subsequent re-aggregation in the presence of cells from different origins to form kidney chimeras. Initially, MSCs did show expression of some genes involved in renal development; however, neither mouse nor human cells expressed important renal development genes, such as Wt1 and Pax2. Accordingly, MSCs were demonstrated to have low renogenic potential in the chimeric kidney model as they did not engraft into ureteric buds, the precursors of collecting duct system, and were only occasionally found in the condensing metanephric mesenchyme, which gives rise to nephrons. In addition, the incorporation of MSCs into embryonic kidneys had some detrimental effect on metanephric development. This effect was mediated through a paracrine action of the cells, as conditioned medium derived from mouse MSCs was demonstrate to reduce ureteric bud branching in in vitro kidney rudiment culture. On the contrary, mouse neonatal kidney cells did engraft into the condensing mesenchyme of chimeric kidneys and were subsequently found in some developing nephron-like structures. Regarding the potential of mouse embryonic stem cells to contribute to renal development in the re-aggregated kidney chimeras, the cells were found to some extent in both the condensing mesenchyme and the laminin-positive tubular compartment of chimeric kidneys, possibly the ureteric buds. No negative effect on kidney development was observed using the neonatal kidney cells as well as the embryonic stem cells. Ultimately it has been shown that the pre-conditioning of mouse MSCs with medium derived from mouse neonatal kidney cells facilitated the engraftment of MSCs into condensing mesenchyme of chimeric kidneys. It also prevented the negative action of MSCs on kidney development confirmed in the in vitro kidney rudiment culture. MSCs were demonstrated to up-regulate GDNF expression upon the pre-conditioning which is important factor for outgrowth and branching of ureteric buds. In conclusion, although pre-conditioning of the MSCs with medium derived from kidney cells was able to improve considerably the renogenic potential of the cells in the chimeric kidney, MSCs demonstrate a relatively low renogenic potential and for this reason are not good candidates for regenerative approaches aimed at recapitulation of nephrogenesis.